Java ImgLibException.printStackTrace方法代码示例

import net.imglib2.exception.ImgLibException; //导入方法依赖的package包/类
static public final void main(String[] args) {
	try {
		FloatImage fi = new FloatImage(new long[]{10, 10, 10});
		Cursor<FloatType> c = fi.cursor();
		while (c.hasNext()) {
			c.next().set(1);
		}
		IntegralImage ig = new IntegralImage(fi);
		
		RandomAccess<DoubleType> p = ig.randomAccess();
		p.setPosition(new long[]{9, 9, 9});
		System.out.println("Test integral image passed: " + ((10 * 10 * 10) == p.get().get()));
		
		new ImageJ();
		ImgLib.show(ig, "Integral Image");
	} catch (ImgLibException e) {
		e.printStackTrace();
	}
}
 

import net.imglib2.exception.ImgLibException; //导入方法依赖的package包/类
/** Copy the contents from img to an ImagePlus; assumes containers are compatible. */
static public ImagePlus copyToFloatImagePlus(final Img<? extends RealType<?>> img, final String title) {
	ImagePlusImgFactory<FloatType> factory = new ImagePlusImgFactory<FloatType>();
	ImagePlusImg<FloatType, ?> iml = factory.create(img, new FloatType());
	Cursor<FloatType> c1 = iml.cursor();
	Cursor<? extends RealType<?>> c2 = img.cursor();
	while (c1.hasNext()) {
		c1.fwd();
		c2.fwd();
		c1.get().set(c2.get().getRealFloat());
	}
	try {
		ImagePlus imp = iml.getImagePlus();
		imp.setTitle(title);
		return imp;
	} catch (ImgLibException e) {
		e.printStackTrace();
		return null;
	}
}
 

import net.imglib2.exception.ImgLibException; //导入方法依赖的package包/类
@Test
public <R extends IntegerType<R> & NativeType<R>> void testIntegralHistogram2d() {
	// Create a 2d image with values 0-9 in every dimension, so bottom right is 81.
	Img<UnsignedByteType> img =
			new UnsignedByteType().createSuitableNativeImg(
					new ArrayImgFactory<UnsignedByteType>(),
					new long[]{10, 10});
	long[] p = new long[2];
	Cursor<UnsignedByteType> c = img.cursor();
	while (c.hasNext()) {
		c.fwd();
		c.localize(p);
		c.get().setInteger(p[0] * p[1]);
	}
	// Create integral histogram with 10 bins
	LinearHistogram<UnsignedByteType> lh = new LinearHistogram<UnsignedByteType>(10, 2, new UnsignedByteType(0), new UnsignedByteType(81));
	Img<R> ih = IntegralHistogram.create(img, lh);
	new ImageJ();
	try {
		ImgLib.wrap((Img)ih, "histogram").show();
	} catch (ImgLibException e) {
		e.printStackTrace();
	}
}
 

import net.imglib2.exception.ImgLibException; //导入方法依赖的package包/类
@SuppressWarnings("rawtypes")
public static final Image< FloatType > wrap( final Img< net.imglib2.type.numeric.real.FloatType > i )
{
	if ( i instanceof ImagePlusImg )
	{
		try
		{
			return ImageJFunctions.wrapFloat( ((ImagePlusImg) i).getImagePlus() );
		}
		catch (ImgLibException e)
		{
			// TODO Auto-generated catch block
			e.printStackTrace();
			return null;
		}			
	}
	else
	{
		return ImgLib2.wrapFloatToImgLib1( i );
	}
}
 

import net.imglib2.exception.ImgLibException; //导入方法依赖的package包/类
public static < T extends NumericType< T > & NativeType< T > > ImagePlus copyToImageStack( final RealRandomAccessible< T > rai, final Interval itvl )
{
	final long[] dimensions = new long[ itvl.numDimensions() ];
	itvl.dimensions( dimensions );

	// create the image plus image
	final T t = rai.realRandomAccess().get();
	final ImagePlusImgFactory< T > factory = new ImagePlusImgFactory< T >();
	final ImagePlusImg< T, ? > target = factory.create( itvl, t );

	double k = 0;
	final long N = dimensions[ 0 ] * dimensions[ 1 ] * dimensions[ 2 ];

	final net.imglib2.Cursor< T > c = target.cursor();
	final RealRandomAccess< T > ra = rai.realRandomAccess();
	while ( c.hasNext() )
	{
		c.fwd();
		ra.setPosition( c );
		c.get().set( ra.get() );

		if ( k % 10000 == 0 )
		{
			IJ.showProgress( k / N );
		}
		k++;
	}

	IJ.showProgress( 1.1 );
	try
	{
		return target.getImagePlus();
	}
	catch ( final ImgLibException e )
	{
		e.printStackTrace();
	}

	return null;
}
 

import net.imglib2.exception.ImgLibException; //导入方法依赖的package包/类
public static void main(String[] args) {
	
	Img<UnsignedByteType> img = ImgLib.wrap(IJ.openImage("/home/albert/Desktop/t2/bridge.gif"));
	
	Img<UnsignedByteType> multiPeriodic =
		new ROI<UnsignedByteType>(
			new ExtendPeriodic<UnsignedByteType>(img),
			new long[]{-512, -512},
			new long[]{1024, 1024});
	
	Img<UnsignedByteType> multiMirroredDouble =
		new ROI<UnsignedByteType>(
			new ExtendMirrorDouble<UnsignedByteType>(img),
			new long[]{-512, -512},
			new long[]{1024, 1024});
	
	Img<UnsignedByteType> multiMirroredSingle =
		new ROI<UnsignedByteType>(
			new ExtendMirrorSingle<UnsignedByteType>(img),
			new long[]{-512, -512},
			new long[]{1024, 1024});
	Img<UnsignedByteType> centered =
		new ROI<UnsignedByteType>(
				new Extend<UnsignedByteType>(img, 0),
				new long[]{-512, -512},
				new long[]{1024, 1024});
	
	// Above, notice the negative offsets. This needs fixing, it's likely due to recent change
	// in how offsets are used. TODO
	
	try {
		ImgLib.show(multiPeriodic, "periodic");
		ImgLib.show(multiMirroredDouble, "mirror double edge");
		ImgLib.show(multiMirroredSingle, "mirror single edge");
		ImgLib.show(centered, "translated 0 background");
	} catch (ImgLibException e) {
		e.printStackTrace();
	}
}
 

import net.imglib2.exception.ImgLibException; //导入方法依赖的package包/类
public ExampleIntegralImageFeatures() throws ImgIOException {
	// Open an image
	String src = "/home/albert/lab/TEM/abd/microvolumes/Seg/180-220-int/180-220-int-00.tif"; // 2d
	final Img<UnsignedByteType> img = (Img<UnsignedByteType>) new ImgOpener().openImgs(src).get(0);
	
	// Integral image
	final Img<LongType> integralImg = new FastIntegralImg<UnsignedByteType, LongType>(img, new LongType(), new IdentityConverter<UnsignedByteType, LongType>());
	// Integral image of squares
	final Img<LongType> integralImgSq = new FastIntegralImg<UnsignedByteType, LongType>(img, new LongType(), new SquaringConverter<UnsignedByteType, LongType>());
	
	// Size of the window
	final long[] radius = new long[integralImg.numDimensions()];
	for (int d=0; d<radius.length; ++d) radius[d] = 5;
	
	// Cursors
	final IntegralCursor<LongType> c1 = new IntegralCursor<LongType>(integralImg, radius);
	final IntegralCursor<LongType> c2 = new IntegralCursor<LongType>(integralImgSq, radius);
	
	// View features
	final long NUM_FEATURES = 4;
	final long[] dims = new long[integralImg.numDimensions() + 1];
	for (int d = 0; d<dims.length -1; ++d) dims[d] = integralImg.dimension(d);
	dims[dims.length -1] = NUM_FEATURES;
	final Img<FloatType> featureStack = new FloatType().createSuitableNativeImg(
			new ArrayImgFactory<FloatType>(), dims);
	final RandomAccess<FloatType> cf = featureStack.randomAccess();
	
	while (c1.hasNext()) {
		final Pair<LongType, long[]> sum = c1.next();
		final Pair<LongType, long[]> sumSq = c2.next();
		cf.setPosition(c1);
		// 1. The sum
		cf.setPosition(0, dims.length -1);
		cf.get().set(sum.getA().getRealFloat());
		// 2. The sum of squares
		cf.fwd(dims.length -1);
		cf.get().set(sumSq.getA().getRealFloat());
		// 3. The mean
		cf.fwd(dims.length -1);
		cf.get().set(sum.getA().getRealFloat() / sum.getB()[0]);
		// 4. The stdDev
		cf.fwd(dims.length -1);
		cf.get().set((float)((sumSq.getA().getRealFloat() - (Math.pow(sum.getA().getRealFloat(), 2) / sum.getB()[0])) / sum.getB()[0]));
	}
	
	try {
		new ImageJ();
		ImgLib.wrap(featureStack).show();
	} catch (ImgLibException e) {
		e.printStackTrace();
	}
}
 

import net.imglib2.exception.ImgLibException; //导入方法依赖的package包/类
@Test
public <R extends IntegerType<R> & NativeType<R>> void testIntegralHistogram1d() {
	// Create a 1d image with values 0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7
	Img<UnsignedByteType> img =
			new UnsignedByteType().createSuitableNativeImg(
					new ArrayImgFactory<UnsignedByteType>(), new long[]{16});
	Cursor<UnsignedByteType> c = img.cursor();
	int i = 0;
	int next = 0;
	while (c.hasNext()) {
		c.fwd();
		c.get().set(next);
		++i;
		if (0 == i % 2) ++next;
	}
	//
	LinearHistogram<UnsignedByteType> lh = new LinearHistogram<UnsignedByteType>(16, 1, new UnsignedByteType(0), new UnsignedByteType(7));
	Img<R> ih = IntegralHistogram.create(img, lh);
	
	new ImageJ();
	try {
		ImgLib.wrap((Img)ih, "histogram").show();
	} catch (ImgLibException e) {
		e.printStackTrace();
	}
	
	RandomAccess<R> ra = ih.randomAccess();
	long[] position = new long[2];
	StringBuilder sb = new StringBuilder();
	for (int k=0; k<ih.dimension(0); ++k) {
		position[0] = k;
		sb.append(k + " :: {");
		for (int h=0; h<ih.dimension(1); ++h) {
			position[1] = h;
			ra.setPosition(position);
			System.out.println(ra.get().getRealDouble());
			sb.append(h).append(':').append((long)ra.get().getRealDouble()).append("; ");
		}
		sb.append("}\n");
	}
	System.out.println(sb.toString());
}
 

import net.imglib2.exception.ImgLibException; //导入方法依赖的package包/类
final static public void main( final String[] args )
	{
		long t;

//		final int[] samples = new int[ m ];
//		final double[][] coordinates = new double[ m ][ 2 ];
		
//		createPhyllotaxis1( samples, coordinates, size[ 0 ] / 2.0, size[ 1 ] / 2.0, 0.1 );
//		createPattern2( samples, coordinates, size[ 0 ] / 2.0, size[ 1 ] / 2.0, 20 );
		
//		final RealPointSampleList< UnsignedShortType > list = new RealPointSampleList< UnsignedShortType >( 2 );
//		for ( int i = 0; i < samples.length; ++i )
//			list.add( new RealPoint( coordinates[ i ] ), new UnsignedShortType( samples[ i ] ) );

		final RealPointSampleList< UnsignedShortType > list = new RealPointSampleList< UnsignedShortType >( 3 );

		createPhyllotaxis2( list, m, size[ 0 ] / 2.0, size[ 1 ] / 2.0, 20 );

		final ImagePlusImgFactory< UnsignedShortType > factory = new ImagePlusImgFactory< UnsignedShortType >();

		final KDTree< UnsignedShortType > kdtree = new KDTree< UnsignedShortType >( list );

		new ImageJ();

		
		IJ.log( "KDTree Search" );
		IJ.log( "=============" );
		
		/* nearest neighbor */
		IJ.log( "Nearest neighbor ..." );
		final ImagePlusImg< UnsignedShortType, ? > img4 = factory.create( new long[]{ size[ 0 ], size[ 1 ], 2 }, new UnsignedShortType() );
		t = drawNearestNeighbor(
				img4,
				new NearestNeighborSearchOnKDTree< UnsignedShortType >( kdtree ) );
		
		IJ.log( t + "ms " );
		
		try
		{
			final ImagePlus imp4 = img4.getImagePlus();
			imp4.setOpenAsHyperStack( true );
			final CompositeImage impComposite = new CompositeImage( imp4, CompositeImage.COMPOSITE );
			impComposite.show();
			impComposite.setSlice( 1 );
			IJ.run( impComposite, "Grays", "" );
			impComposite.setDisplayRange( 0, m - 1 );
			impComposite.setSlice( 2 );
			impComposite.setDisplayRange( 0, 2 );
			impComposite.updateAndDraw();
			IJ.log( "Done." );
		}
		catch ( final ImgLibException e )
		{
			IJ.log( "Didn't work out." );
			e.printStackTrace();
		}
	}